Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 51
Found at i:3094464 original size:24 final size:25
Alignment explanation
Indices: 3094406--3094464 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
3094396 AAATATAAAT
*
3094406 AATTATTAAGATATTCAATAAATTA
1 AATTATTAAAATATTCAATAAATTA
*
3094431 AA-TATAAAAATATT-AA-AAGATTA
1 AATTATTAAAATATTCAATAA-ATTA
3094454 AATTATTAAAA
1 AATTATTAAAA
3094465 GAATTAATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 2 0.07
23 8 0.28
24 17 0.59
25 2 0.07
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (25 bp):
AATTATTAAAATATTCAATAAATTA
Found at i:3095634 original size:32 final size:31
Alignment explanation
Indices: 3095590--3095675 Score: 127
Period size: 32 Copynumber: 2.7 Consensus size: 31
3095580 CCGGTTAAAA
*
3095590 TTTGGTTTGGGTTAATTTCGGTTCAGTTTGC
1 TTTGGTTTGGGTTAATTTCGATTCAGTTTGC
*
3095621 TTTCGGTTTGGGTTAATTTCGATTCGGTTTGC
1 TTT-GGTTTGGGTTAATTTCGATTCAGTTTGC
* *
3095653 TTTTGTTCGGGTTAATTTCGATT
1 TTTGGTTTGGGTTAATTTCGATT
3095676 TCGGTTCAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 21 0.42
32 29 0.58
ACGTcount: A:0.10, C:0.10, G:0.27, T:0.52
Consensus pattern (31 bp):
TTTGGTTTGGGTTAATTTCGATTCAGTTTGC
Found at i:3095640 original size:16 final size:16
Alignment explanation
Indices: 3095588--3095641 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
3095578 TTCCGGTTAA
3095588 AATTT-GGTTTGGGTT
1 AATTTCGGTTTGGGTT
** *
3095603 AATTTCGGTTCAGTTT
1 AATTTCGGTTTGGGTT
**
3095619 GCTTTCGGTTTGGGTT
1 AATTTCGGTTTGGGTT
3095635 AATTTCG
1 AATTTCG
3095642 ATTCGGTTTG
Statistics
Matches: 28, Mismatches: 10, Indels: 1
0.72 0.26 0.03
Matches are distributed among these distances:
15 5 0.18
16 23 0.82
ACGTcount: A:0.13, C:0.09, G:0.28, T:0.50
Consensus pattern (16 bp):
AATTTCGGTTTGGGTT
Found at i:3095647 original size:37 final size:38
Alignment explanation
Indices: 3095604--3095698 Score: 96
Period size: 31 Copynumber: 2.7 Consensus size: 38
3095594 GTTTGGGTTA
*
3095604 ATTTCGGTTCAGTTTGCTTTCGGTTTGGGTTAATTTCG
1 ATTTCGGTTCAGTTTGCTTTCAGTTTGGGTTAATTTCG
* *
3095642 A-TTC-G----GTTTGCTTT-TGTTCGGGTTAATTTCG
1 ATTTCGGTTCAGTTTGCTTTCAGTTTGGGTTAATTTCG
* *
3095673 ATTTCGGTTCAGATTGATTTCAGTTT
1 ATTTCGGTTCAGTTTGCTTTCAGTTT
3095699 CCCTAAATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
31 16 0.36
32 12 0.27
33 1 0.02
36 1 0.02
37 10 0.23
38 4 0.09
ACGTcount: A:0.13, C:0.13, G:0.24, T:0.51
Consensus pattern (38 bp):
ATTTCGGTTCAGTTTGCTTTCAGTTTGGGTTAATTTCG
Found at i:3097385 original size:18 final size:19
Alignment explanation
Indices: 3097364--3097438 Score: 68
Period size: 18 Copynumber: 4.2 Consensus size: 19
3097354 GACTAGTTTT
*
3097364 ACCCAG-TTTGACTCGTTG
1 ACCCAGATTTGACCCGTTG
3097382 ACCC-GATTTGACCCGTTG
1 ACCCAGATTTGACCCGTTG
***
3097400 ACCCA-ACCCGACCCGTTG
1 ACCCAGATTTGACCCGTTG
**
3097418 ACCCA-ACCTGACCCGTTG
1 ACCCAGATTTGACCCGTTG
3097436 ACC
1 ACC
3097439 GTTGACTTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
17 1 0.02
18 49 0.98
ACGTcount: A:0.20, C:0.40, G:0.19, T:0.21
Consensus pattern (19 bp):
ACCCAGATTTGACCCGTTG
Found at i:3104529 original size:18 final size:19
Alignment explanation
Indices: 3104506--3104553 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
3104496 AGTGGACTAG
*
3104506 TTGACCCGTTGAG-TCGGT
1 TTGACCCGTTGAGCCCGGT
3104524 TTGACCCGTTG-GCCCGGT
1 TTGACCCGTTGAGCCCGGT
3104542 TTGACCCGTTGA
1 TTGACCCGTTGA
3104554 TCTGGTCTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.10, C:0.27, G:0.31, T:0.31
Consensus pattern (19 bp):
TTGACCCGTTGAGCCCGGT
Found at i:3104611 original size:18 final size:18
Alignment explanation
Indices: 3104560--3104613 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
3104550 TTGATCTGGT
3104560 CTAACCTGACCCGTTGAC
1 CTAACCTGACCCGTTGAC
** **
3104578 CCGACC-GACCTATTGAC
1 CTAACCTGACCCGTTGAC
3104595 CTAACCTGACCCGTTGAC
1 CTAACCTGACCCGTTGAC
3104613 C
1 C
3104614 GTTGACTTTG
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.22, C:0.41, G:0.17, T:0.20
Consensus pattern (18 bp):
CTAACCTGACCCGTTGAC
Found at i:3105304 original size:7 final size:7
Alignment explanation
Indices: 3105292--3105333 Score: 84
Period size: 7 Copynumber: 6.0 Consensus size: 7
3105282 TATTGTTTTG
3105292 ACATGAT
1 ACATGAT
3105299 ACATGAT
1 ACATGAT
3105306 ACATGAT
1 ACATGAT
3105313 ACATGAT
1 ACATGAT
3105320 ACATGAT
1 ACATGAT
3105327 ACATGAT
1 ACATGAT
3105334 TTCTGAATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (7 bp):
ACATGAT
Found at i:3110523 original size:90 final size:90
Alignment explanation
Indices: 3110367--3110544 Score: 275
Period size: 90 Copynumber: 2.0 Consensus size: 90
3110357 CCTAACACAC
* * * ** *
3110367 CCTTTTATAGCCAAGTTACCCTAGTCATATTAGGGTTTTTATTATTTTGAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATATAT
* *
3110432 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
*
3110457 CCTTTTATATCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATATAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATATAT
3110522 ATTTAATTAATTGAAATTAAATA
66 ATTTAATTAATTGAAATTAAATA
3110545 TTTGGGATTA
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.45
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATCAGGGATTTTATTATTTCAAATTAATTAAATATAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:3110531 original size:20 final size:21
Alignment explanation
Indices: 3110506--3110574 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
3110496 TATTATTTCA
3110506 AATTAATT-AAATATATATTT
1 AATTAATTAAAATATATATTT
* *
3110526 AATTAATTGAAATTAAATATTT
1 AATTAATT-AAAATATATATTT
* *
3110548 GGGATT-ATTAAAATATATACTT
1 --AATTAATTAAAATATATATTT
3110570 AATTA
1 AATTA
3110575 GCTCTAGATA
Statistics
Matches: 37, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 11 0.30
22 20 0.54
23 3 0.08
24 3 0.08
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (21 bp):
AATTAATTAAAATATATATTT
Found at i:3112226 original size:25 final size:25
Alignment explanation
Indices: 3112173--3112248 Score: 116
Period size: 25 Copynumber: 3.0 Consensus size: 25
3112163 AAATACTTTA
*
3112173 GGTCATTTTACACTTTAAGGGCATTTT
1 GGTCATTTT-CACTTT-AGAGCATTTT
3112200 GGTCATTTTCACTTTAGAGCATTTT
1 GGTCATTTTCACTTTAGAGCATTTT
*
3112225 GGTCATTTTCACTTTAAAGCATTT
1 GGTCATTTTCACTTTAGAGCATTT
3112249 ATATAAATCT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
25 32 0.68
26 6 0.13
27 9 0.19
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.46
Consensus pattern (25 bp):
GGTCATTTTCACTTTAGAGCATTTT
Found at i:3113184 original size:14 final size:14
Alignment explanation
Indices: 3113165--3113214 Score: 82
Period size: 14 Copynumber: 3.6 Consensus size: 14
3113155 AATCGTACGA
3113165 GTTGACTCAGACGG
1 GTTGACTCAGACGG
*
3113179 GTTGACTGAGACGG
1 GTTGACTCAGACGG
*
3113193 GTTGACTCAGACGA
1 GTTGACTCAGACGG
3113207 GTTGACTC
1 GTTGACTC
3113215 GGTGAATGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24
Consensus pattern (14 bp):
GTTGACTCAGACGG
Found at i:3118337 original size:19 final size:19
Alignment explanation
Indices: 3118313--3118360 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
3118303 AAAACCCGAT
3118313 GGGGGTATCGGTACCGCTA
1 GGGGGTATCGGTACCGCTA
**
3118332 GGGGGTATAAGTACCGCTA
1 GGGGGTATCGGTACCGCTA
3118351 GGGGGTATCG
1 GGGGGTATCG
3118361 ATACACATTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.19, C:0.17, G:0.44, T:0.21
Consensus pattern (19 bp):
GGGGGTATCGGTACCGCTA
Found at i:3118388 original size:23 final size:23
Alignment explanation
Indices: 3118355--3118418 Score: 119
Period size: 23 Copynumber: 2.8 Consensus size: 23
3118345 CCGCTAGGGG
*
3118355 GTATCGATACACATTCAATGAAT
1 GTATCGGTACACATTCAATGAAT
3118378 GTATCGGTACACATTCAATGAAT
1 GTATCGGTACACATTCAATGAAT
3118401 GTATCGGTACACATTCAA
1 GTATCGGTACACATTCAA
3118419 GGTGTATCGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (23 bp):
GTATCGGTACACATTCAATGAAT
Found at i:3122166 original size:20 final size:21
Alignment explanation
Indices: 3122130--3122169 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3122120 GAAGCTTTAA
*
3122130 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTTTTGAT
3122151 GATCATC-ATTTACTTTTGA
1 GATCATCAATTTACTTTTGA
3122170 AAGTAAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.25, C:0.15, G:0.10, T:0.50
Consensus pattern (21 bp):
GATCATCAATTTACTTTTGAT
Found at i:3129075 original size:24 final size:23
Alignment explanation
Indices: 3129047--3129094 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 23
3129037 AAATATGTTG
3129047 TTTATTATT-TACATTATAATATTA
1 TTTATTATTATACATTA-AAT-TTA
3129071 TTTATTATTATACATTAAATTTA
1 TTTATTATTATACATTAAATTTA
3129094 T
1 T
3129095 GTGTCGAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.17
24 12 0.52
25 7 0.30
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTATTATTATACATTAAATTTA
Found at i:3130525 original size:31 final size:31
Alignment explanation
Indices: 3130481--3130546 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
3130471 ACTCGGGGTA
*
3130481 ACCACATATTAATTAAATAAAAACGAAAGTG
1 ACCACATAGTAATTAAATAAAAACGAAAGTG
*
3130512 ACCACATCGTAATTAAATAAAAACGAAAGTG
1 ACCACATAGTAATTAAATAAAAACGAAAGTG
3130543 ACCA
1 ACCA
3130547 TATCTTATGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.53, C:0.17, G:0.11, T:0.20
Consensus pattern (31 bp):
ACCACATAGTAATTAAATAAAAACGAAAGTG
Found at i:3133518 original size:12 final size:12
Alignment explanation
Indices: 3133501--3133525 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3133491 CCCTTTATCG
3133501 CTCGGACCACCA
1 CTCGGACCACCA
3133513 CTCGGACCACCA
1 CTCGGACCACCA
3133525 C
1 C
3133526 CCACGGTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.52, G:0.16, T:0.08
Consensus pattern (12 bp):
CTCGGACCACCA
Found at i:3135765 original size:5 final size:5
Alignment explanation
Indices: 3135757--3136507 Score: 1277
Period size: 5 Copynumber: 149.6 Consensus size: 5
3135747 AAATAAAAGT
* * * * * * * *
3135757 ATAAC ATAAC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
* * * * * * * * * *
3135807 ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC ATAGC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
* * * *
3135857 ATATC ATAAC ATAGC ATAGC ATAGC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
3135907 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
3135957 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
3136007 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAACAC ATAAC ATAAC ATAAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC AT-A-AC ATAAC ATAAC AT-AAC
3136060 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
3136110 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
3136160 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
3136210 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
3136260 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
3136310 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
3136360 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
3136410 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC
3136460 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATA
1 ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATAAC ATA
3136508 CGTATTAAAC
Statistics
Matches: 738, Mismatches: 5, Indels: 6
0.99 0.01 0.01
Matches are distributed among these distances:
5 727 0.99
6 7 0.01
7 4 0.01
ACGTcount: A:0.57, C:0.20, G:0.03, T:0.20
Consensus pattern (5 bp):
ATAAC
Found at i:3136595 original size:2 final size:2
Alignment explanation
Indices: 3136584--3136744 Score: 74
Period size: 2 Copynumber: 83.5 Consensus size: 2
3136574 ATTTTTAAAA
* *
3136584 AT AT AT -T AT AT A- AT AT -T AT AT TT AT A- AT ACT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * *
3136623 AT AT TT AT TT AT AT AT AT ACT AT AT A- AC AT AT A- AT AA AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* * * *
3136664 AT TT A- AT AA AT AT AT -T AT AT AA AT ACT AT ACT AT AT AT A- AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A-T AT AT AT AT AT
* * * *
3136705 AC AT AA AT ACC AT AT AT AT A- AT AT AT A- AT AT AT AA AT AT A
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3136745 CCATAATATA
Statistics
Matches: 118, Mismatches: 25, Indels: 32
0.67 0.14 0.18
Matches are distributed among these distances:
1 11 0.09
2 98 0.83
3 9 0.08
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3136672 original size:13 final size:12
Alignment explanation
Indices: 3136654--3136688 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
3136644 ATATAACATA
3136654 TAATAAATATATT
1 TAATAAATATA-T
3136667 TAATAAATATAT
1 TAATAAATATAT
3136679 TATATAAATA
1 TA-ATAAATA
3136689 CTATACTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 3 0.14
13 18 0.86
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TAATAAATATAT
Found at i:3136728 original size:7 final size:7
Alignment explanation
Indices: 3136718--3136766 Score: 53
Period size: 7 Copynumber: 6.4 Consensus size: 7
3136708 TAAATACCAT
3136718 ATATATA
1 ATATATA
3136725 ATATATA
1 ATATATA
3136732 ATATATAA
1 ATATAT-A
3136740 ATATACCATA
1 ATAT---ATA
*
3136750 ATATAAA
1 ATATATA
3136757 ATATATA
1 ATATATA
3136764 ATA
1 ATA
3136767 AAACACTACT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
7 24 0.67
8 5 0.14
10 5 0.14
11 2 0.06
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (7 bp):
ATATATA
Found at i:3136750 original size:18 final size:18
Alignment explanation
Indices: 3136711--3136761 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 18
3136701 TAAAACATAA
3136711 ATACCAT-ATATAT-AAT
1 ATACCATAATATATAAAT
3136727 AT---ATAATATATAAAT
1 ATACCATAATATATAAAT
3136742 ATACCATAATATA-AAAT
1 ATACCATAATATATAAAT
3136759 ATA
1 ATA
3136762 TAATAAAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 2 0.07
14 6 0.20
15 5 0.17
16 2 0.07
17 7 0.23
18 8 0.27
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (18 bp):
ATACCATAATATATAAAT
Found at i:3137689 original size:56 final size:56
Alignment explanation
Indices: 3137603--3137711 Score: 182
Period size: 56 Copynumber: 1.9 Consensus size: 56
3137593 CCCTTCATAG
*
3137603 TGAAGTTGAAATTCGAATTAAAGATCTTGATTAGAAATAGCTCCTCATTGTAGTCT
1 TGAAGTTGAAATTCGAATTAAAGATCTTGATTAGAAATAGCTCATCATTGTAGTCT
* * *
3137659 TGAAGTTGAAATTCGACTTGAAGATCTTGATTGGAAATAGCTCATCATTGTAG
1 TGAAGTTGAAATTCGAATTAAAGATCTTGATTAGAAATAGCTCATCATTGTAG
3137712 AGTTGAGCTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (56 bp):
TGAAGTTGAAATTCGAATTAAAGATCTTGATTAGAAATAGCTCATCATTGTAGTCT
Found at i:3152119 original size:12 final size:12
Alignment explanation
Indices: 3152102--3152132 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3152092 ATTTTCTTGT
3152102 TCCTCAATGAAG
1 TCCTCAATGAAG
3152114 TCCTCAATGAAG
1 TCCTCAATGAAG
3152126 TCCTCAA
1 TCCTCAA
3152133 GATGTCGTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (12 bp):
TCCTCAATGAAG
Found at i:3157743 original size:2 final size:2
Alignment explanation
Indices: 3157738--3157771 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3157728 ATAAAAAAAC
3157738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3157772 TTACATGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3159239 original size:106 final size:106
Alignment explanation
Indices: 3159102--3159888 Score: 936
Period size: 106 Copynumber: 7.4 Consensus size: 106
3159092 AAAGTTTTGC
* * * * ** * * *
3159102 TGTCTCGGGTCCAATATCCTTCGCTGTGAAGTTGAAATAGGTTCCAAAACTGGGTAGTTGTTTGT
1 TGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGT
** *
3159167 TGACAACAAGTCACCCCTTCGTTGTGAAGTTGAGCTTGTGT
66 TGACAACAAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGT
* * * * *
3159208 TGCCTCGAGTCCAATATCTTTCGCTATGAAGTTGAAATTGGCTCTAAAATTGGGAAATTGTTTGT
1 TGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGT
* * * *
3159273 TGATAACCAGTCGTCCGTTCGTTTTGAAGTTGAACTTGTGT
66 TGACAACAAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGT
* *
3159314 TGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAGTTGGCTCTGAAATTGGGAAATTGTTTGT
1 TGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGT
*
3159379 TGACAACCA-TCCGTCCCTTCGTTGTGAAGTTGAACTTGTGT
66 TGACAACAAGT-CGTCCCTTCGTTGTGAAGTTGAACTTGTGT
*
3159420 TGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGT
1 TGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGT
* * * *
3159485 TGACAGCCAA-CCGTCCCTTC-TCTGTGAAGTTGAGCTTGTGC
66 TGACA-ACAAGTCGTCCCTTCGT-TGTGAAGTTGAACTTGTGT
* * * * ** *
3159526 TGTCTCGAGTCTAATATCCTTCGATGTGAAGTTGAAATTGACCCTGAAACTAAGAAATGGTTTGT
1 TGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGT
*
3159591 TGACAA-ACAGACGTCCCTTCGTTGTGAAGTTGAACTTGTGT
66 TGACAACA-AGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGT
* * *
3159632 TGTCTCGAGTCCAATATCCTTTGTTATGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGT
1 TGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGT
* * * ** * *
3159697 TGACAGCCAA-CCGCCCCTTCACTGTGAAGTTGAGCTTGTGC
66 TGACA-ACAAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGT
* * ** * * *
3159738 TGTCTCGAGTCTAATATCCTTCGATGTGAGGTTGAAATTAACCCTGAAACTGGGAAATAGTTTGT
1 TGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGT
* * * *
3159803 TAACAACCAGACGTCCCTTCGTTATGAAGTTGAACTTGTGT
66 TGACAACAAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGT
* * * *
3159844 TGTCTCGAGTCTATTATTCTTCGATGTGAAGTTGAAATTGACTCT
1 TGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCT
3159889 AGCTAAAACT
Statistics
Matches: 586, Mismatches: 86, Indels: 18
0.85 0.12 0.03
Matches are distributed among these distances:
104 1 0.00
105 5 0.01
106 575 0.98
107 4 0.01
108 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (106 bp):
TGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGT
TGACAACAAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGT
Found at i:3159472 original size:212 final size:211
Alignment explanation
Indices: 3159099--3159888 Score: 1060
Period size: 212 Copynumber: 3.7 Consensus size: 211
3159089 TGAAAAGTTT
* * * ** * * *
3159099 TGCTGTCTCGGGTCCAATATCCTTCGCTGTGAAGTTGAAATAGGTTCC-AAAACTGGGTAGTTGT
1 TGCTGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAAT-TGACCCTGAAACTGGGAAATTGT
* * ** * * *
3159163 TTGTTGACAACAAGTCACCCCTTCGTTGTGAAGTTGAGCTTGTGTTGCCTCGAGTCCAATATCTT
65 TTGTTGACAACCAGACGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCT
* * * * ** *
3159228 TCGCTATGAAGTTGAAATTGGCTCTAAAATTGGGAAATTGTTTGTTGATAACCAGTCGTCCGTTC
130 TCGTTATGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAGCCAACCGTCCCTTC
* *
3159293 GTTTTGAAGTTGAACTTG
195 -TTGTGAAGTTGAGCTTG
* * * * * *
3159311 TGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAGTTGGCTCTGAAATTGGGAAATTGTT
1 TGCTGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACCCTGAAACTGGGAAATTGTT
**
3159376 TGTTGACAACCATCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTT
66 TGTTGACAACCAGACGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTT
*
3159441 CGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAGCCAACCGTCCCTTCT
131 CGTTATGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAGCCAACCGTCCCTTCT
3159506 CTGTGAAGTTGAGCTTG
196 -TGTGAAGTTGAGCTTG
* ** *
3159523 TGCTGTCTCGAGTCTAATATCCTTCGATGTGAAGTTGAAATTGACCCTGAAACTAAGAAATGGTT
1 TGCTGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACCCTGAAACTGGGAAATTGTT
*
3159588 TGTTGACAAACAGACGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTT
66 TGTTGACAACCAGACGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTT
* *
3159653 TGTTATGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAGCCAACCGCCCCTTCA
131 CGTTATGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAGCCAACCGTCCCTTC-
*
3159718 CTGTGAAGTTGAGCTTG
195 TTGTGAAGTTGAGCTTG
* * * *
3159735 TGCTGTCTCGAGTCTAATATCCTTCGATGTGAGGTTGAAATTAACCCTGAAACTGGGAAATAGTT
1 TGCTGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACCCTGAAACTGGGAAATTGTT
* * * * *
3159800 TGTTAACAACCAGACGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCTCGAGTCTATTATTCTT
66 TGTTGACAACCAGACGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTT
* * *
3159865 CGATGTGAAGTTGAAATTGACTCT
131 CGTTATGAAGTTGAAATTGGCTCT
3159889 AGCTAAAACT
Statistics
Matches: 513, Mismatches: 62, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
211 3 0.01
212 510 0.99
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (211 bp):
TGCTGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGACCCTGAAACTGGGAAATTGTT
TGTTGACAACCAGACGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTT
CGTTATGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAGCCAACCGTCCCTTCT
TGTGAAGTTGAGCTTG
Found at i:3159679 original size:318 final size:316
Alignment explanation
Indices: 3159099--3159885 Score: 1038
Period size: 318 Copynumber: 2.5 Consensus size: 316
3159089 TGAAAAGTTT
* * * * ** * *
3159099 TGCTGTCTCGGGTCCAATATCCTTCGCTGTGAAGTTGAAATAGGTTCCAAAACTGGGTAGTTGTT
1 TGCTGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTT
* * * *
3159164 TGTTGACAACAA-GTCACCCCTTCGTTGTGAAGTTGAGCTTGTGTTGCCTCGAGTCCAATATCTT
66 TGTTGACACCAACGT---CCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATATCCT
* * * * * ** * * * * *
3159228 TCGCTATGAAGTTGAAATTGGCTCTAAAATTGGGAAATTGTTTGTTGATAACCAGTCGTCCGTTC
128 TCGATGTGAAGTTGAAATTGACCCTAAAACTAAGAAATGGTTTGTTGACAAACAGACGTCCCTTC
* * *
3159293 GTTTTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAGTTGGCTC
193 GTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTC
* * **
3159358 TGAAATTGGGAAATTGTTTGTTGACAACCATCCGTCCCTTCGTTGTGAAGTTGAACTTG
258 TGAAATTGGGAAATTGTTTGTTGACAACCAACCGCCCCTTCACTGTGAAGTTGAACTTG
* * *
3159417 TGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTT
1 TGCTGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTT
*
3159482 TGTTGACAGCCAACCGTCCCTTC-TCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATATCCT
66 TGTTGACA-CCAA-CGTCCCTTCGT-TGTGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATATCCT
*
3159546 TCGATGTGAAGTTGAAATTGACCCTGAAACTAAGAAATGGTTTGTTGACAAACAGACGTCCCTTC
128 TCGATGTGAAGTTGAAATTGACCCTAAAACTAAGAAATGGTTTGTTGACAAACAGACGTCCCTTC
*
3159611 GTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTTGTTATGAAGTTGAAATTGGCTC
193 GTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTC
* *
3159676 TGAAATTGGGAAATTGTTTGTTGACAGCCAACCGCCCCTTCACTGTGAAGTTGAGCTTG
258 TGAAATTGGGAAATTGTTTGTTGACAACCAACCGCCCCTTCACTGTGAAGTTGAACTTG
* * ** * *
3159735 TGCTGTCTCGAGTCTAATATCCTTCGATGTGAGGTTGAAATTAACCCTGAAACTGGGAAATAGTT
1 TGCTGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTT
* * * * *
3159800 TGTTAACAACCAGACGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCTCGAGTCTATTATTCTT
66 TGTTGAC-ACCA-ACGTCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATATCCTT
3159865 CGATGTGAAGTTGAAATTGAC
129 CGATGTGAAGTTGAAATTGAC
3159886 TCTAGCTAAA
Statistics
Matches: 409, Mismatches: 53, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
317 1 0.00
318 400 0.98
319 6 0.01
321 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (316 bp):
TGCTGTCTCGAGTCCAATATCCTTCGATGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTGTT
TGTTGACACCAACGTCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCTAATATCCTTCG
ATGTGAAGTTGAAATTGACCCTAAAACTAAGAAATGGTTTGTTGACAAACAGACGTCCCTTCGTT
GTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGA
AATTGGGAAATTGTTTGTTGACAACCAACCGCCCCTTCACTGTGAAGTTGAACTTG
Found at i:3160320 original size:37 final size:37
Alignment explanation
Indices: 3160244--3160322 Score: 88
Period size: 37 Copynumber: 2.1 Consensus size: 37
3160234 TGAGAAACAA
* * * **
3160244 TCTCAAGGGAGACAAAATTTTGTTTTAAGAAAAACTG
1 TCTCAAGAGAGACAAAACTTAGTTCCAAGAAAAACTG
*
3160281 TCTCAAGAGAGACAAAACTTAGTTCCAA-AAGAAATTG
1 TCTCAAGAGAGACAAAACTTAGTTCCAAGAA-AAACTG
3160318 TCTCA
1 TCTCA
3160323 CGGGGAGATG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
36 2 0.06
37 33 0.94
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (37 bp):
TCTCAAGAGAGACAAAACTTAGTTCCAAGAAAAACTG
Found at i:3160471 original size:35 final size:35
Alignment explanation
Indices: 3160432--3160500 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 35
3160422 TCAATATTTA
**
3160432 TGTTTCAAGAGAAACTTTTTCAAAGGTTTTTTTTG
1 TGTTTCAAGAGAAACGATTTCAAAGGTTTTTTTTG
3160467 TGTTTCAAGAGAAACGATTTCAAAGGTTTTTTTT
1 TGTTTCAAGAGAAACGATTTCAAAGGTTTTTTTT
3160501 CTAAGGGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.28, C:0.09, G:0.17, T:0.46
Consensus pattern (35 bp):
TGTTTCAAGAGAAACGATTTCAAAGGTTTTTTTTG
Found at i:3161079 original size:18 final size:18
Alignment explanation
Indices: 3161052--3161087 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3161042 TGTTGAATCC
*
3161052 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
3161070 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
3161088 TTCATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:3161504 original size:22 final size:22
Alignment explanation
Indices: 3161478--3161532 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
3161468 TTATGTTTGG
*
3161478 TCAAAGGTTTGGCATTTGATGT
1 TCAAAGGTTTGGCATTTGATGC
3161500 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
3161522 TCAAAGGTTTG
1 TCAAAGGTTTG
3161533 ATGGGGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:3162162 original size:17 final size:17
Alignment explanation
Indices: 3162142--3162183 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3162132 TTTGTACCTT
3162142 TTTCTTTTTTATTC-TTG
1 TTTCTTTTTT-TTCTTTG
*
3162159 TTTCTCTTTTTTCTTTG
1 TTTCTTTTTTTTCTTTG
3162176 TTT-TTTTT
1 TTTCTTTTT
3162184 CTTTTTGCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81
Consensus pattern (17 bp):
TTTCTTTTTTTTCTTTG
Found at i:3167556 original size:106 final size:106
Alignment explanation
Indices: 3167371--3167951 Score: 732
Period size: 106 Copynumber: 5.5 Consensus size: 106
3167361 ATCTGGAAAG
* * * * * * * * *
3167371 TTGTGCTGTCTCGGGTCCAATATCCTTCGCTGTGAAGTTTAAATTGGTTCCGAAACTGGGTAGTT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
* *
3167436 GTTTGTTGACAACCAGTCGCCCCTTCCTTGTGAAGTTGAGC
66 GTTTGTTGACAACCAGTCGTCCCTTCCTTGTGAAGTTGAAC
* * *
3167477 TTGTGTTGCCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
*
3167542 GTTTGTTGACAACCAGTCGTCCCTTCATTGTGAAGTTGAAC
66 GTTTGTTGACAACCAGTCGTCCCTTCCTTGTGAAGTTGAAC
* * * *
3167583 TTGTGTTGTCTCGAGTCCAATATCCTTCATTGTGAAGTTGAAGTTGGCTCTAAAATTAGGAAATT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
*
3167648 GTTTGTTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAAC
66 GTTTGTTGACAACCAGTCGTCCCTTCCTTGTGAAGTTGAAC
* * *
3167689 TTATGTTGTCTCGAGTCCAATATCCTTCGTTATGAAGTTGAAATTGGCTTTGAAATTGGGAAATT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
* ** * * *
3167754 GTTTGTTGACAGCCAAACGCCCCTTCGC-TATGAAGTTGAGC
66 GTTTGTTGACAACCAGTCGTCCCTTC-CTTGTGAAGTTGAAC
* * * * * * * *
3167795 TTGTGCTGTCTCGAGTCTAATATCCTTCGATGTGAAGTTGAAATTGACCCTAAAACTGGGAAATA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
* * * * *
3167860 ATTTGCTAACAACCAGACGTCCCTTCGTTGTGAAGTTGAAC
66 GTTTGTTGACAACCAGTCGTCCCTTCCTTGTGAAGTTGAAC
** * *
3167901 TTGTGTTGTCTCGAGTATAATATTCTTCGTTGTGAAGTTGAAATTGACTCT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
3167952 AGCTAAAACT
Statistics
Matches: 413, Mismatches: 60, Indels: 4
0.87 0.13 0.01
Matches are distributed among these distances:
106 413 1.00
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (106 bp):
TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
GTTTGTTGACAACCAGTCGTCCCTTCCTTGTGAAGTTGAAC
Found at i:3168538 original size:34 final size:34
Alignment explanation
Indices: 3168495--3168561 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
3168485 TCAATGTTTA
**
3168495 TGTTTCAAGAGAAACTTTTTCAAAGGTTTTTTTG
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTG
3168529 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTT
1 TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTT
3168562 TTCTAAGGGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (34 bp):
TGTTTCAAGAGAAACAATTTCAAAGGTTTTTTTG
Found at i:3169142 original size:18 final size:18
Alignment explanation
Indices: 3169115--3169150 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3169105 TGTTTAATCC
*
3169115 CCAAAGATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
3169133 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
3169151 TTCATGTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.33, G:0.08, T:0.17
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:3169567 original size:22 final size:22
Alignment explanation
Indices: 3169541--3169595 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
3169531 TTATGTTTGG
*
3169541 TCAAAGGTTTGGCATTTGATGT
1 TCAAAGGTTTGGCATTTGATGC
3169563 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
3169585 TCAAAGGTTTG
1 TCAAAGGTTTG
3169596 ATGGGGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:3175262 original size:106 final size:106
Alignment explanation
Indices: 3175063--3175697 Score: 817
Period size: 106 Copynumber: 6.0 Consensus size: 106
3175053 AGCTGAAAAG
* * * * * * * *
3175063 TTGTGCTGTCTCGGGTCCAATATCCCTCGTTGTGAAGTTGAAATTGGTTCCGAAACTGGGTAGTT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
* *** * ** * *
3175128 GTTTGTTTACATTTAGTCACCCCTTCGTTGTGAAGTTGAGC
66 GTTTGTTGACAACCAGACGTCCCTTCGCTGTGAAGTTGAAC
* * * *
3175169 TTCTGTTGCCTCGAGTCCAATATCTTTCGTTGTGAAGTTAAAATTGGCTCTGAAATTGGGAAATT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
* * *
3175234 GTTTGTTGACAACCAGTCGTCCCTTCGTTATGAAGTTGAAC
66 GTTTGTTGACAACCAGACGTCCCTTCGCTGTGAAGTTGAAC
* * * * *
3175275 TTGTGTTCTCTCGAGTCCAATATACTTCGTTGTGAAGTTGAAGTTAGCTCTGAAATTAGGAAATT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
3175340 GTTTGTTGACAACCAGACGTCCCTTCGCTGTGAAGTTGAAC
66 GTTTGTTGACAACCAGACGTCCCTTCGCTGTGAAGTTGAAC
*
3175381 TTGTGTTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
* *
3175446 TTTTGTTGACAGCCA-ACCGTCCCTTCGCTGTGAAGTT-AACC
66 GTTTGTTGACAACCAGA-CGTCCCTTCGCTGTGAAGTTGAA-C
* * * * * * * * *
3175487 TTGTGCTGTCTCGAGTCTAATATCCTTCGATATGAAGTTGAAATTGACCCTGAAACTAGGAAATG
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
*
3175552 GTTTGTTGACAACCAGACGTCCCTTCGTTGTGAAGTTGAAC
66 GTTTGTTGACAACCAGACGTCCCTTCGCTGTGAAGTTGAAC
3175593 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
* * *
3175658 GTTTGTTGAC-AGCAAACCGCCCCTTCGCTGTGAAGTTGAA
66 GTTTGTTGACAACCAGA-CGTCCCTTCGCTGTGAAGTTGAA
3175698 ATTGACCCTG
Statistics
Matches: 458, Mismatches: 66, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
105 7 0.02
106 448 0.98
107 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (106 bp):
TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
GTTTGTTGACAACCAGACGTCCCTTCGCTGTGAAGTTGAAC
Found at i:3175745 original size:63 final size:63
Alignment explanation
Indices: 3175616--3175757 Score: 178
Period size: 63 Copynumber: 2.3 Consensus size: 63
3175606 AGTCCAATAT
* * * * * *
3175616 CCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAGCAAACCGCC
1 CCTTCGTTGTGAAGTTGAAATTGACCCTGAAACTGGGAAATGGTTTGTTGAAACCAAACCGCC
* * *
3175679 CCTTCGCTGTGAAGTTGAAATTGACCCTGAAACTGGGAAATGGTTTTTTGATAACCAAA-CGTC
1 CCTTCGTTGTGAAGTTGAAATTGACCCTGAAACTGGGAAATGGTTTGTTGA-AACCAAACCGCC
*
3175742 CCTTCATTGTGAAGTT
1 CCTTCGTTGTGAAGTT
3175758 AAGCTTGTGT
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
63 62 0.93
64 5 0.07
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (63 bp):
CCTTCGTTGTGAAGTTGAAATTGACCCTGAAACTGGGAAATGGTTTGTTGAAACCAAACCGCC
Found at i:3176244 original size:37 final size:37
Alignment explanation
Indices: 3176162--3176246 Score: 91
Period size: 37 Copynumber: 2.3 Consensus size: 37
3176152 TTTTCATGAG
* * * * **
3176162 AAACAGTCTCAAGGGAGACAAAATTTTGTTTTAAGAA
1 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
3176199 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAA-AA
1 AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
*
3176235 GAAATTGTCTCA
1 -AAACTGTCTCA
3176247 CGGGGAGATG
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 2 0.05
37 38 0.95
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (37 bp):
AAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAGAA
Found at i:3176399 original size:34 final size:34
Alignment explanation
Indices: 3176356--3176422 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
3176346 TCAATGTTTA
**
3176356 TGTTTCAAGAGAAACTTTTTCAAAGGTTTTTTTG
1 TGTTTCAAGAGAAACGATTTCAAAGGTTTTTTTG
*
3176390 TGTTTCAAGAGAAACGATTTCAAATGTTTTTTT
1 TGTTTCAAGAGAAACGATTTCAAAGGTTTTTTT
3176423 TCTAAGGGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.46
Consensus pattern (34 bp):
TGTTTCAAGAGAAACGATTTCAAAGGTTTTTTTG
Found at i:3178687 original size:2 final size:2
Alignment explanation
Indices: 3178682--3178733 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
3178672 AAAAACACAC
3178682 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3178724 AT AT AT AT AT
1 AT AT AT AT AT
3178734 GTACATGATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3190466 original size:18 final size:18
Alignment explanation
Indices: 3190443--3190498 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 18
3190433 GGCGCATAGA
*
3190443 ATGTCCCGTAGGACCACT
1 ATGTCCCGAAGGACCACT
3190461 ATGTCCCGAAGGACCACTGTAT
1 ATGTCCCGAAGGACCAC----T
3190483 ATGTCCCGAAGGACCA
1 ATGTCCCGAAGGACCA
3190499 TTGTATATCC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
18 16 0.48
22 17 0.52
ACGTcount: A:0.27, C:0.30, G:0.23, T:0.20
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:3190488 original size:22 final size:22
Alignment explanation
Indices: 3190460--3190506 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
3190450 GTAGGACCAC
3190460 TATGTCCCGAAGGACCACTGTA
1 TATGTCCCGAAGGACCACTGTA
*
3190482 TATGTCCCGAAGGACCATTGTA
1 TATGTCCCGAAGGACCACTGTA
3190504 TAT
1 TAT
3190507 CCCTCAACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (22 bp):
TATGTCCCGAAGGACCACTGTA
Found at i:3193679 original size:19 final size:20
Alignment explanation
Indices: 3193636--3193683 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
3193626 TACTAGGCTG
* *
3193636 GAAATTAATGTTAGAGTGTT
1 GAAATTGATGTTAGAATGTT
3193656 GAAATTGATGTTAGAATG-T
1 GAAATTGATGTTAGAATGTT
3193675 GAAATTGAT
1 GAAATTGAT
3193684 CAATTTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGTT
Found at i:3194874 original size:22 final size:21
Alignment explanation
Indices: 3194837--3194879 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3194827 TATTATATAC
*
3194837 GATGTTTATCATGAATACATAT
1 GATGTTTATCAAGAATA-ATAT
*
3194859 GATGTTTATTAAGAATAATAT
1 GATGTTTATCAAGAATAATAT
3194880 TTTGGGTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.40, C:0.05, G:0.14, T:0.42
Consensus pattern (21 bp):
GATGTTTATCAAGAATAATAT
Found at i:3195156 original size:27 final size:27
Alignment explanation
Indices: 3195097--3195159 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
3195087 TGAAGTTGAG
*
3195097 GAAAAATCTAGTAAATCGGAACGAATA
1 GAAAATTCTAGTAAATCGGAACGAATA
3195124 GAAAATTCTAGTAAATCGGAACGAATA
1 GAAAATTCTAGTAAATCGGAACGAATA
3195151 GAAAATTCT
1 GAAAATTCT
3195160 TGAAAATCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.22
Consensus pattern (27 bp):
GAAAATTCTAGTAAATCGGAACGAATA
Found at i:3195166 original size:27 final size:27
Alignment explanation
Indices: 3195097--3195167 Score: 106
Period size: 27 Copynumber: 2.6 Consensus size: 27
3195087 TGAAGTTGAG
* *
3195097 GAAAAATCTAGTAAATCGGAACGAATA
1 GAAAATTCTAGAAAATCGGAACGAATA
*
3195124 GAAAATTCTAGTAAATCGGAACGAATA
1 GAAAATTCTAGAAAATCGGAACGAATA
*
3195151 GAAAATTCTTGAAAATC
1 GAAAATTCTAGAAAATC
3195168 TAAAGGATGA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.23
Consensus pattern (27 bp):
GAAAATTCTAGAAAATCGGAACGAATA
Found at i:3196130 original size:30 final size:30
Alignment explanation
Indices: 3196090--3196156 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
3196080 AGCCTTAGAG
* *
3196090 AAATTTGGGGACC-ATT-ATGTAATTTTTGA
1 AAATTAGGGGACCAATTCAT-TAATTTTGGA
3196119 AAAGTTAGGGGACCAATTCATTAATTTTGGA
1 AAA-TTAGGGGACCAATTCATTAATTTTGGA
3196150 AAATTAG
1 AAATTAG
3196157 TGAATGGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 3 0.09
30 13 0.39
31 15 0.45
32 2 0.06
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (30 bp):
AAATTAGGGGACCAATTCATTAATTTTGGA
Found at i:3197684 original size:17 final size:18
Alignment explanation
Indices: 3197652--3197685 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3197642 GCTTTTATTA
*
3197652 TTATTATATTAAAATAAT
1 TTATTATATAAAAATAAT
3197670 TTATT-TATAAAAATAA
1 TTATTATATAAAAATAA
3197686 AATTTTACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTATTATATAAAAATAAT
Found at i:3199298 original size:15 final size:15
Alignment explanation
Indices: 3199274--3199313 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
3199264 AGCCAAAAAG
3199274 AAACAAAATATAATA
1 AAACAAAATATAATA
* *
3199289 AAACACAATATTATA
1 AAACAAAATATAATA
3199304 AAACAAAATA
1 AAACAAAATA
3199314 AACATTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (15 bp):
AAACAAAATATAATA
Found at i:3205635 original size:20 final size:21
Alignment explanation
Indices: 3205598--3205636 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3205588 TAAGGCATTA
3205598 AAAATCATAAACAAAACAAAT
1 AAAATCATAAACAAAACAAAT
*
3205619 AAAATCATACA-AAAACAA
1 AAAATCATAAACAAAACAA
3205637 TCATTCGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.72, C:0.15, G:0.00, T:0.13
Consensus pattern (21 bp):
AAAATCATAAACAAAACAAAT
Found at i:3205880 original size:26 final size:26
Alignment explanation
Indices: 3205845--3205932 Score: 122
Period size: 26 Copynumber: 3.3 Consensus size: 26
3205835 ACTATGAACT
3205845 GCCTCAGCTCGCTAGCTCCTCTCGGAC
1 GCCT-AGCTCGCTAGCTCCTCTCGGAC
* * * *
3205872 GTCTAGCTCACTAGCTTCTCTCAGAC
1 GCCTAGCTCGCTAGCTCCTCTCGGAC
*
3205898 GCCTAGCTCGCTAGCTCCTCTTGGAC
1 GCCTAGCTCGCTAGCTCCTCTCGGAC
3205924 GCCTAGCTC
1 GCCTAGCTC
3205933 ACCACTCCAT
Statistics
Matches: 52, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
26 49 0.94
27 3 0.06
ACGTcount: A:0.14, C:0.40, G:0.20, T:0.26
Consensus pattern (26 bp):
GCCTAGCTCGCTAGCTCCTCTCGGAC
Found at i:3206985 original size:22 final size:22
Alignment explanation
Indices: 3206960--3207004 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
3206950 ATTGGTAAGA
3206960 AATTTTATATGTGGTTCATATC
1 AATTTTATATGTGGTTCATATC
3206982 AATTTTATATGTGGTTCATATC
1 AATTTTATATGTGGTTCATATC
3207004 A
1 A
3207005 TGTTAATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (22 bp):
AATTTTATATGTGGTTCATATC
Found at i:3208649 original size:37 final size:37
Alignment explanation
Indices: 3208588--3208660 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 37
3208578 AGGATAATTG
* * *
3208588 GAAAATGTTACATCATTGTCGACAACATTCCTGGGTA
1 GAAAATGTTACAACATTCTCGACAAAATTCCTGGGTA
* * *
3208625 GAAAATGTTGCAACATTCTGGACAAAATTCTTGGGT
1 GAAAATGTTACAACATTCTCGACAAAATTCCTGGGT
3208661 GTAGACAAGG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (37 bp):
GAAAATGTTACAACATTCTCGACAAAATTCCTGGGTA
Found at i:3209166 original size:20 final size:21
Alignment explanation
Indices: 3209133--3209171 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
3209123 CTTATTTAGC
*
3209133 ATGAGTTTGCTTTGGATGATT
1 ATGAGTTTGCTTTGAATGATT
*
3209154 ATGA-TTTGTTTTGAATGA
1 ATGAGTTTGCTTTGAATGA
3209172 ATGGTTTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.23, C:0.03, G:0.26, T:0.49
Consensus pattern (21 bp):
ATGAGTTTGCTTTGAATGATT
Found at i:3218160 original size:17 final size:17
Alignment explanation
Indices: 3218134--3218166 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3218124 CCCTAAATTA
3218134 ATTTCATCAAAATATAT
1 ATTTCATCAAAATATAT
*
3218151 ATTTCCTCAAAATATA
1 ATTTCATCAAAATATA
3218167 GGGTTTGGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTTCATCAAAATATAT
Found at i:3221456 original size:21 final size:21
Alignment explanation
Indices: 3221413--3221456 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
3221403 GTTTCATTAC
* *
3221413 AGGAATTCATGGCCTCGATAA
1 AGGAATTCATGGCCTCAACAA
* *
3221434 AGGATTTCATGGCTTCAACAA
1 AGGAATTCATGGCCTCAACAA
3221455 AG
1 AG
3221457 ACACTGATGC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (21 bp):
AGGAATTCATGGCCTCAACAA
Found at i:3226798 original size:551 final size:552
Alignment explanation
Indices: 3225750--3226854 Score: 1845
Period size: 551 Copynumber: 2.0 Consensus size: 552
3225740 AGGAATACAA
* *
3225750 AGGAGCACCAGTCATGCGCGACAAACCGACATCAACAACACATGATGCCCAAGAGTTTTCCTTAC
1 AGGAGCACCAGTCATGCACGACAAACCGACATCAACAACACATGATGCCCAAGAGTTTTCCTTAA
*
3225815 TTACCTTAACATAATTCGTTGCCTAGGCAACGAAAATCTTAATTTTGTACGTAAATAAATTAAGT
66 TTACCTTAACACAATTCGTTGCCTAGGCAACGAAAATCTTAATTTTGTACGTAAATAAATTAAGT
*
3225880 TATTTTATGCACTAGTTATATGTTTTACTTTATTTATGTTTTTTTATATTTATTGCAAGCATGCA
131 TATTTTATGCACTAGTTATATGTTTTACTTTATTTATGTTCTTTTATATTTATTGCAAGCATGCA
*
3225945 TGGTACATGTGGCAGAATGGGGTGAGAACTTACACATGAAAGGAAGAGAAACCCTAGAGCAAAGG
196 TGGTACATGTGGCAGAATGGGGTGAGAACTTACACATGAAAGGAAGAGAAACCCTAGAGCAAAAG
* *
3226010 AGGTTTTGGCGGCAATTGTAAAGAGGAAAACTATCTTTTCCCCACTTTATGTTTAATCAAATATT
261 AGGTTTTGGCGGCAATTGTAAAGAGGAAAACTATCTTTTCCCCACTTTACGTCTAATCAAATATT
* * * *
3226075 GAGAATTTAAAGTCATATCTTTTCCCTTATCATTTTGAGCAAATTGCCCTGTAGAAACAACCTAT
326 GAGAATTCAAAGTCATATCTTTTCCCCTATCATTTTGAGCAAATTGCCCTGAAGAAACAACCCAT
* * *
3226140 TAACTTTCTAGAAAAACCAACTTCAACTTCATCTTCATCATTATGCATTATTTTCTCTCATTCAA
391 TAACTTTCCAGAAAAACCAACTTCAACTCCATCTTCATCATCATGCATTATTTTCTCTCATTCAA
*
3226205 AAAAATTCCCTTCAAAAACATCCCCCATCGCCGTCGCAAAACACATTGTACCAACGAGTATCATA
456 AAAAATTCCCTTCAAAAACATCCCCCATCGCCGTCACAAAACACATTGTACCAACGAGTATCATA
*
3226270 GCTAGATTGAAGAAAAACCCATCCCCAACACC
521 GCTAGATCGAAGAAAAACCCATCCCCAACACC
* *
3226302 AGGAGCACCAGTCATGCACGACAAACCGACATCAACAGCATATGATGCCCAAGAGTTTTCCTTAA
1 AGGAGCACCAGTCATGCACGACAAACCGACATCAACAACACATGATGCCCAAGAGTTTTCCTTAA
* * * *
3226367 TTACCTTAACACAATTTGTTGCTTAGGCAATGAAAATCTTAATTTTGTACGTAAATAAATTTAGT
66 TTACCTTAACACAATTCGTTGCCTAGGCAACGAAAATCTTAATTTTGTACGTAAATAAATTAAGT
* * *
3226432 TATTTTATGCACTAGTTATCTGTTTTACTTTATTTCTGTTCTTTT-TATTTATTGCAGGCATGCA
131 TATTTTATGCACTAGTTATATGTTTTACTTTATTTATGTTCTTTTATATTTATTGCAAGCATGCA
*
3226496 TGGTACATGTGGCAGCATGGGGTGAGAACTTACACATGAAAGGAAGAGAAACCCTAGAGCAAAAG
196 TGGTACATGTGGCAGAATGGGGTGAGAACTTACACATGAAAGGAAGAGAAACCCTAGAGCAAAAG
* * *
3226561 AGGTTTTGGCGGCAGTTGTAAAGAGGGAAACTATCTTTTCCCCACTTTACGTCTAATGAAATATT
261 AGGTTTTGGCGGCAATTGTAAAGAGGAAAACTATCTTTTCCCCACTTTACGTCTAATCAAATATT
* * *
3226626 GAGCATTCAATGTCATATC-TTTCCCCTATCATTTTGAGCAAATTGCCCTGAAGAAACCACCCAT
326 GAGAATTCAAAGTCATATCTTTTCCCCTATCATTTTGAGCAAATTGCCCTGAAGAAACAACCCAT
* *
3226690 TAACTTTCCAGAAAACCCAACTTCAACTCCATCTTCATCATCATGCTTTATTTTCTCTCATTCAA
391 TAACTTTCCAGAAAAACCAACTTCAACTCCATCTTCATCATCATGCATTATTTTCTCTCATTC-A
* **
3226755 AAAAAATTCCCTTCAAAAACTTCCTTCATCGCCGTCACAAAACACATTGTACCAACGAGTATCAT
455 AAAAAATTCCCTTCAAAAACATCCCCCATCGCCGTCACAAAACACATTGTACCAACGAGTATCAT
*
3226820 GGCTAGATCGAAGAAAAACCCATCCCCAACACC
520 AGCTAGATCGAAGAAAAACCCATCCCCAACACC
3226853 AG
1 AG
3226855 ACTTTGAGCA
Statistics
Matches: 514, Mismatches: 38, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
550 99 0.19
551 252 0.49
552 163 0.32
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (552 bp):
AGGAGCACCAGTCATGCACGACAAACCGACATCAACAACACATGATGCCCAAGAGTTTTCCTTAA
TTACCTTAACACAATTCGTTGCCTAGGCAACGAAAATCTTAATTTTGTACGTAAATAAATTAAGT
TATTTTATGCACTAGTTATATGTTTTACTTTATTTATGTTCTTTTATATTTATTGCAAGCATGCA
TGGTACATGTGGCAGAATGGGGTGAGAACTTACACATGAAAGGAAGAGAAACCCTAGAGCAAAAG
AGGTTTTGGCGGCAATTGTAAAGAGGAAAACTATCTTTTCCCCACTTTACGTCTAATCAAATATT
GAGAATTCAAAGTCATATCTTTTCCCCTATCATTTTGAGCAAATTGCCCTGAAGAAACAACCCAT
TAACTTTCCAGAAAAACCAACTTCAACTCCATCTTCATCATCATGCATTATTTTCTCTCATTCAA
AAAAATTCCCTTCAAAAACATCCCCCATCGCCGTCACAAAACACATTGTACCAACGAGTATCATA
GCTAGATCGAAGAAAAACCCATCCCCAACACC
Found at i:3238566 original size:35 final size:36
Alignment explanation
Indices: 3238520--3238601 Score: 139
Period size: 35 Copynumber: 2.3 Consensus size: 36
3238510 ACTCCCCCTT
*
3238520 ACTTTTAACACTTCTCCCATTTATCATTTA-AAAAC
1 ACTTTTAACACTTCTCCCATTTAGCATTTAGAAAAC
3238555 ACTTTTAACACTTCTCCCATTTAGCATTTAGAAAAC
1 ACTTTTAACACTTCTCCCATTTAGCATTTAGAAAAC
*
3238591 ACATTTAACAC
1 ACTTTTAACAC
3238602 CATTTAACAC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
35 29 0.66
36 15 0.34
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (36 bp):
ACTTTTAACACTTCTCCCATTTAGCATTTAGAAAAC
Found at i:3240923 original size:23 final size:21
Alignment explanation
Indices: 3240893--3240950 Score: 75
Period size: 23 Copynumber: 2.8 Consensus size: 21
3240883 TCCCCTGTGG
3240893 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTTCCCC-TC-AA
3240916 GGGGGAATCGGTT-CCCTCAA
1 GGGGGAATCGGTTCCCCTCAA
*
3240936 GGGGG-ATCGATTCCC
1 GGGGGAATCGGTTCCC
3240951 TCTGCACTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 6 0.18
20 9 0.27
21 2 0.06
22 3 0.09
23 13 0.39
ACGTcount: A:0.19, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCCTCAA
Found at i:3248794 original size:28 final size:27
Alignment explanation
Indices: 3248752--3248812 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 27
3248742 ATATTCCTTT
* *
3248752 CTTTTCTTTCATTTCATTGTTCTTAAAC
1 CTTTTCCTTCATTTCATT-TCCTTAAAC
*
3248780 CTTTTCCTTCTTTTCATTTCCTTAAAC
1 CTTTTCCTTCATTTCATTTCCTTAAAC
*
3248807 CATTTC
1 CTTTTC
3248813 TTTTAGCTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 13 0.45
28 16 0.55
ACGTcount: A:0.16, C:0.26, G:0.02, T:0.56
Consensus pattern (27 bp):
CTTTTCCTTCATTTCATTTCCTTAAAC
Found at i:3255392 original size:24 final size:24
Alignment explanation
Indices: 3255363--3255415 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
3255353 TCATAAAATG
3255363 GAGGCTAAAATCATGAAGATATAT
1 GAGGCTAAAATCATGAAGATATAT
*
3255387 GAGGCTTAAATCATGAAGATATAT
1 GAGGCTAAAATCATGAAGATATAT
3255411 GAGGC
1 GAGGC
3255416 AAGCACCATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.09, G:0.25, T:0.25
Consensus pattern (24 bp):
GAGGCTAAAATCATGAAGATATAT
Found at i:3259295 original size:24 final size:24
Alignment explanation
Indices: 3259268--3259319 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
3259258 TCATAAAATG
3259268 GAGGCTAAAATCATGAAGATATAT
1 GAGGCTAAAATCATGAAGATATAT
*
3259292 GAGGCTTAAATCATGAAGATATAT
1 GAGGCTAAAATCATGAAGATATAT
3259316 GAGG
1 GAGG
3259320 TAAGCACCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.25
Consensus pattern (24 bp):
GAGGCTAAAATCATGAAGATATAT
Found at i:3264550 original size:5 final size:5
Alignment explanation
Indices: 3264531--3264566 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
3264521 ATATCAATAC
* *
3264531 ATAAT ATTAT ATAAT GTAAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A
3264567 ATATTAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (5 bp):
ATAAT
Found at i:3264592 original size:16 final size:16
Alignment explanation
Indices: 3264554--3264600 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
3264544 ATGTAATATA
*
3264554 ATATAATATAATAATATT
1 ATATTATAT-ATAA-ATT
3264572 A-ATTATATATAAATT
1 ATATTATATATAAATT
3264587 ATATTATATATAAA
1 ATATTATATATAAA
3264601 ATGTACTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 4 0.15
16 16 0.59
17 6 0.22
18 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATTATATATAAATT
Found at i:3264598 original size:20 final size:19
Alignment explanation
Indices: 3264531--3264633 Score: 61
Period size: 18 Copynumber: 6.0 Consensus size: 19
3264521 ATATCAATAC
*
3264531 ATAATATTATATA-ATGTA
1 ATAATATTATATATATATA
3264549 AT-ATA--ATATA-ATATA
1 ATAATATTATATATATATA
3264564 ATAATATTA-AT-TATAT-
1 ATAATATTATATATATATA
3264580 ATAA-ATTATATTATATATA
1 ATAATATTATA-TATATATA
* *
3264599 A-AAT-GTACTATATATGTA
1 ATAATATTA-TATATATATA
*
3264617 AT-ATA-TAAATATATATA
1 ATAATATTATATATATATA
3264634 TGTCATGCTA
Statistics
Matches: 68, Mismatches: 5, Indels: 25
0.69 0.05 0.26
Matches are distributed among these distances:
15 15 0.22
16 8 0.12
17 18 0.26
18 24 0.35
19 3 0.04
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (19 bp):
ATAATATTATATATATATA
Found at i:3264610 original size:16 final size:16
Alignment explanation
Indices: 3264575--3264613 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3264565 TAATATTAAT
* *
3264575 TATATATAAATTATAT
1 TATATATAAAATATAC
*
3264591 TATATATAAAATGTAC
1 TATATATAAAATATAC
3264607 TATATAT
1 TATATAT
3264614 GTAATATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (16 bp):
TATATATAAAATATAC
Found at i:3264621 original size:11 final size:11
Alignment explanation
Indices: 3264531--3264859 Score: 78
Period size: 10 Copynumber: 30.7 Consensus size: 11
3264521 ATATCAATAC
3264531 ATAATAT-TAT
1 ATAATATATAT
*
3264541 ATAATGTA-AT
1 ATAATATATAT
3264551 ATAATATA-AT
1 ATAATATATAT
3264561 ATAATA-ATAT
1 ATAATATATAT
3264571 -TAAT-TATAT
1 ATAATATATAT
3264580 ATAA-AT-TAT
1 ATAATATATAT
*
3264589 ATTATATATAAAAT
1 A-TA-ATAT-ATAT
* *
3264603 GTACTATATAT
1 ATAATATATAT
* *
3264614 GTAATATATAA
1 ATAATATATAT
3264625 AT-ATATATAT
1 ATAATATATAT
* * * *
3264635 GTCATGCTACAT
1 ATAAT-ATATAT
3264647 ATAATATAT-T
1 ATAATATATAT
3264657 ATAAT-T-TAT
1 ATAATATATAT
3264666 ATAAT-T-TAT
1 ATAATATATAT
* * *
3264675 -TATTTTGT-T
1 ATAATATATAT
* * *
3264684 AAAACAATAAAT
1 ATAA-TATATAT
* * *
3264696 GTAATATTTTT
1 ATAATATATAT
* *
3264707 AGAAATATGCTAT
1 A-TAATAT-ATAT
3264720 ATAATAT-TAT
1 ATAATATATAT
3264730 AT-ATATATAT
1 ATAATATATAT
3264740 ATATATATATAT
1 ATA-ATATATAT
3264752 ATATATATATAT
1 ATA-ATATATAT
3264764 ACTAA-ATA-AT
1 A-TAATATATAT
* * *
3264774 GTAAAATAAAT
1 ATAATATATAT
* * *
3264785 ATTATTTATAA
1 ATAATATATAT
3264796 ATACCATAT-TAT
1 ATA--ATATATAT
*
3264808 AT-ATATA-AC
1 ATAATATATAT
3264817 ATGAATACTATAT
1 AT-AATA-TATAT
3264830 AT-ATATAATAT
1 ATAATAT-ATAT
*
3264841 ATAA-ATATACC
1 ATAATATATA-T
3264852 ATAATATA
1 ATAATATA
3264860 AAATAAATAA
Statistics
Matches: 234, Mismatches: 48, Indels: 72
0.66 0.14 0.20
Matches are distributed among these distances:
8 4 0.02
9 40 0.17
10 66 0.28
11 52 0.22
12 57 0.24
13 13 0.06
14 2 0.01
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.43
Consensus pattern (11 bp):
ATAATATATAT
Found at i:3264732 original size:2 final size:2
Alignment explanation
Indices: 3264717--3264849 Score: 86
Period size: 2 Copynumber: 69.0 Consensus size: 2
3264707 AGAAATATGC
3264717 TA TA TA -A TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
3264757 TA TA TA TA CTA AA TA -A TG TA -A AA TA AA TA T- TA TT TA TA AA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
3264797 TA CCA TA T- TA TA TA TA TA -A CA TGA -A TA CTA TA TA TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA TA T-A TA TA -TA TA TA TA TA TA
*
3264837 -A TA TA TA AA TA TA
1 TA TA TA TA TA TA TA
3264850 CCATAATATA
Statistics
Matches: 102, Mismatches: 16, Indels: 26
0.71 0.11 0.18
Matches are distributed among these distances:
1 9 0.09
2 87 0.85
3 6 0.06
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (2 bp):
TA
Found at i:3264864 original size:25 final size:26
Alignment explanation
Indices: 3264821--3264869 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
3264811 TATAACATGA
* * *
3264821 ATACTATATATATATAATATATAAAT
1 ATACCATATATATAAAATAAATAAAT
3264847 ATACCATA-ATATAAAATAAATAA
1 ATACCATATATATAAAATAAATAA
3264870 TAAAATACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 13 0.65
26 7 0.35
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (26 bp):
ATACCATATATATAAAATAAATAAAT
Found at i:3270424 original size:2 final size:2
Alignment explanation
Indices: 3270417--3270441 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3270407 TATCTATTAG
3270417 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3270442 TAAGCTACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3274017 original size:17 final size:17
Alignment explanation
Indices: 3273991--3274027 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
3273981 ATACTAAATG
3273991 TATAGCTTACGCTATAT
1 TATAGCTTACGCTATAT
*
3274008 TATAGTTTACGCTATAT
1 TATAGCTTACGCTATAT
3274025 TAT
1 TAT
3274028 TTATCAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.46
Consensus pattern (17 bp):
TATAGCTTACGCTATAT
Found at i:3281217 original size:19 final size:20
Alignment explanation
Indices: 3281183--3281221 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3281173 CTTGGAGTAA
*
3281183 TATTTTTGACATTCGAATAT
1 TATTTTTGACAATCGAATAT
3281203 TATTTTTGA-AATCGAATAT
1 TATTTTTGACAATCGAATAT
3281222 AAAATCTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.49
Consensus pattern (20 bp):
TATTTTTGACAATCGAATAT
Found at i:3290153 original size:27 final size:27
Alignment explanation
Indices: 3290114--3290178 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
3290104 ATACCCTAGC
3290114 TCATT-TAGCTTCAAATACATCCAAAA
1 TCATTCTAGCTTCAAATACATCCAAAA
*
3290140 TCATTCTAGCTTCAAATACATCCCAAA
1 TCATTCTAGCTTCAAATACATCCAAAA
3290167 TCATTCTAGCTT
1 TCATTCTAGCTT
3290179 TCTCCTAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 5 0.14
27 32 0.86
ACGTcount: A:0.35, C:0.26, G:0.05, T:0.34
Consensus pattern (27 bp):
TCATTCTAGCTTCAAATACATCCAAAA
Found at i:3295753 original size:48 final size:48
Alignment explanation
Indices: 3295671--3295770 Score: 155
Period size: 48 Copynumber: 2.1 Consensus size: 48
3295661 AAGTTTGTAG
3295671 CATCTACATCGATAGACGCCTCAGAATTAACCTCCATTTCATCTGCAA
1 CATCTACATCGATAGACGCCTCAGAATTAACCTCCATTTCATCTGCAA
* * * * *
3295719 CATCTACATTGATAGATGCCTCTGGATTAGCCTCCATTTCATCTGCAA
1 CATCTACATCGATAGACGCCTCAGAATTAACCTCCATTTCATCTGCAA
3295767 CATC
1 CATC
3295771 AACAATATCC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.28, C:0.30, G:0.12, T:0.30
Consensus pattern (48 bp):
CATCTACATCGATAGACGCCTCAGAATTAACCTCCATTTCATCTGCAA
Found at i:3306965 original size:67 final size:67
Alignment explanation
Indices: 3306857--3307057 Score: 303
Period size: 67 Copynumber: 3.0 Consensus size: 67
3306847 CCTTAGGTCT
* *
3306857 ATAAGGAATTACCAGTCTATGCTAAACCTATACAAGGAATTACCAGCAGTGACTGAACCTGCCAG
1 ATAAGGAATTACCAGTCGATGCTGAACCTATACAAGGAATTACCAGCAGTGACTGAACCTGCCAG
3306922 AG
66 AG
*** * * *
3306924 ATAAGGAATTACCAGTCGATGCTGAACCTATACAAGGAATTACCAGCAACAACTAAACATGCTAG
1 ATAAGGAATTACCAGTCGATGCTGAACCTATACAAGGAATTACCAGCAGTGACTGAACCTGCCAG
3306989 AG
66 AG
* * *
3306991 ATAAGGAATTACCAGTCGGTGTTGAACCTATATAAGGAATTACCAGCAGTGACTGAACCTGCCAG
1 ATAAGGAATTACCAGTCGATGCTGAACCTATACAAGGAATTACCAGCAGTGACTGAACCTGCCAG
3307056 AG
66 AG
3307058 TCTTCATGCC
Statistics
Matches: 117, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
67 117 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (67 bp):
ATAAGGAATTACCAGTCGATGCTGAACCTATACAAGGAATTACCAGCAGTGACTGAACCTGCCAG
AG
Found at i:3307048 original size:31 final size:31
Alignment explanation
Indices: 3306856--3307050 Score: 121
Period size: 31 Copynumber: 6.0 Consensus size: 31
3306846 ACCTTAGGTC
*
3306856 TATAAGGAATTACCAGTCTA-TGCTAAACCTA
1 TATAAGGAATTACCAGTC-AGTGCTGAACCTA
*
3306887 TACAAGGAATTACCAG-CAGTGACTGAACCTGCCAGA
1 TATAAGGAATTACCAGTCAGTG-CTGAACCT-----A
*
3306923 GATAAGGAATTACCAGTC-GATGCTGAACCTA
1 TATAAGGAATTACCAGTCAG-TGCTGAACCTA
* *** *
3306954 TACAAGGAATTACCAG-CAACAACTAAACATGCTAGA
1 TATAAGGAATTACCAGTC-AGTGCTGAAC---CT--A
* * *
3306990 GATAAGGAATTACCAGTCGGTGTTGAACCTA
1 TATAAGGAATTACCAGTCAGTGCTGAACCTA
3307021 TATAAGGAATTACCAG-CAGTGACTGAACCT
1 TATAAGGAATTACCAGTCAGTG-CTGAACCT
3307051 GCCAGAGTCT
Statistics
Matches: 125, Mismatches: 21, Indels: 36
0.69 0.12 0.20
Matches are distributed among these distances:
29 1 0.01
30 8 0.06
31 65 0.52
33 2 0.02
34 2 0.02
36 43 0.34
37 4 0.03
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (31 bp):
TATAAGGAATTACCAGTCAGTGCTGAACCTA
Found at i:3337996 original size:21 final size:20
Alignment explanation
Indices: 3337972--3338010 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
3337962 TAAAAAGAAA
3337972 AAATAAAACAAAGACAAGACG
1 AAATAAAACAAAGA-AAGACG
**
3337993 AAATTGAACAAAGAAAGA
1 AAATAAAACAAAGAAAGA
3338011 GAAGAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.67, C:0.10, G:0.15, T:0.08
Consensus pattern (20 bp):
AAATAAAACAAAGAAAGACG
Found at i:3338329 original size:17 final size:17
Alignment explanation
Indices: 3338307--3338340 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3338297 AATAATCAAT
3338307 AAAAT-AATTGAAAATTC
1 AAAATAAATT-AAAATTC
3338324 AAAATAAATTAAAATTC
1 AAAATAAATTAAAATTC
3338341 TTGTATTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAATAAATTAAAATTC
Found at i:3340719 original size:19 final size:20
Alignment explanation
Indices: 3340676--3340722 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
3340666 TACTATGCTG
* *
3340676 GAAATTAATGTTAGAGTGTT
1 GAAATTGATGTTAGAATGTT
3340696 GAAATTGATGTTAGAATG-T
1 GAAATTGATGTTAGAATGTT
3340715 GAAATTGA
1 GAAATTGA
3340723 ACCATTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.36
Consensus pattern (20 bp):
GAAATTGATGTTAGAATGTT
Found at i:3341991 original size:22 final size:21
Alignment explanation
Indices: 3341954--3341996 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
3341944 TATTATATAC
*
3341954 GATGTTTATCATGAATACATAT
1 GATGTTTATCACGAATA-ATAT
*
3341976 GATGTTTATTACGAATAATAT
1 GATGTTTATCACGAATAATAT
3341997 TTTGGGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (21 bp):
GATGTTTATCACGAATAATAT
Found at i:3344124 original size:21 final size:21
Alignment explanation
Indices: 3344099--3344177 Score: 83
Period size: 21 Copynumber: 3.7 Consensus size: 21
3344089 TTTTCGTAAG
3344099 AGTACTTCT-TGTACTTGGAGT
1 AGTACTT-TGTGTACTTGGAGT
* *
3344120 AGTACTTAGTG-ACTATGATAAG-
1 AGTACTTTGTGTACT-TG--GAGT
3344142 AGTACTTTGTGTACTTGGAGT
1 AGTACTTTGTGTACTTGGAGT
3344163 AGTACTTTGTGTACT
1 AGTACTTTGTGTACT
3344178 ATGGCACTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
20 5 0.10
21 26 0.54
22 12 0.25
23 5 0.10
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.41
Consensus pattern (21 bp):
AGTACTTTGTGTACTTGGAGT
Found at i:3344156 original size:43 final size:44
Alignment explanation
Indices: 3344095--3344180 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 44
3344085 TGCATTTTCG
3344095 TAAGAGTACTTCTTGTACTTGGAGTAGTACTTAGTG-ACTATGA
1 TAAGAGTACTTCTTGTACTTGGAGTAGTACTTAGTGTACTATGA
*
3344138 TAAGAGTACTT-TGTGTACTTGGAGTAGTACTTTGTGTACTATG
1 TAAGAGTACTTCT-TGTACTTGGAGTAGTACTTAGTGTACTATG
3344181 GCACTTTGTG
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
42 1 0.03
43 33 0.82
44 6 0.15
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (44 bp):
TAAGAGTACTTCTTGTACTTGGAGTAGTACTTAGTGTACTATGA
Found at i:3349790 original size:22 final size:22
Alignment explanation
Indices: 3349765--3349819 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
3349755 CATTTGGGGT
3349765 ATCGATTCCCCTGATACAGGGA
1 ATCGATTCCCCTGATACAGGGA
* *
3349787 ATCGATTCCCTTGCTACAGGGA
1 ATCGATTCCCCTGATACAGGGA
3349809 ATCGATTCCCC
1 ATCGATTCCCC
3349820 CACTGTTCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.25
Consensus pattern (22 bp):
ATCGATTCCCCTGATACAGGGA
Found at i:3352193 original size:15 final size:15
Alignment explanation
Indices: 3352173--3352216 Score: 79
Period size: 15 Copynumber: 2.9 Consensus size: 15
3352163 ATATATTATA
3352173 AGAAGAAGAAAAAAC
1 AGAAGAAGAAAAAAC
*
3352188 AGAAGAAAAAAAAAC
1 AGAAGAAGAAAAAAC
3352203 AGAAGAAGAAAAAA
1 AGAAGAAGAAAAAA
3352217 AATAGAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (15 bp):
AGAAGAAGAAAAAAC
Found at i:3352229 original size:6 final size:6
Alignment explanation
Indices: 3352172--3352262 Score: 64
Period size: 6 Copynumber: 15.3 Consensus size: 6
3352162 TATATATTAT
* * *
3352172 AAGAAG AAGAAA AA-ACAG AAGAAA AA-AAA ACAGAAG AAGAAA AA-AAA
1 AAGAAA AAGAAA AAGA-AA AAGAAA AAGAAA A-AGAAA AAGAAA AAGAAA
* * * *
3352219 TAGAAA AAGAAA ATGAAA ACGAGA AAG-AA AAGAAA AAGAGAA AA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGA-AA AA
3352263 AAATGAGAGA
Statistics
Matches: 66, Mismatches: 12, Indels: 13
0.73 0.13 0.14
Matches are distributed among these distances:
5 13 0.20
6 45 0.68
7 8 0.12
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.02
Consensus pattern (6 bp):
AAGAAA
Found at i:3352231 original size:15 final size:16
Alignment explanation
Indices: 3352173--3352231 Score: 70
Period size: 15 Copynumber: 3.8 Consensus size: 16
3352163 ATATATTATA
3352173 AGAAG-AAGAAAAAAC
1 AGAAGAAAGAAAAAAC
3352188 AGAAGAAA-AAAAAAC
1 AGAAGAAAGAAAAAAC
* *
3352203 AGAAGAAGAAAAAAAAT
1 AGAAGAA-AGAAAAAAC
3352220 AGAA-AAAGAAAA
1 AGAAGAAAGAAAA
3352232 TGAAAACGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
15 24 0.62
16 5 0.13
17 10 0.26
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (16 bp):
AGAAGAAAGAAAAAAC
Found at i:3352247 original size:18 final size:18
Alignment explanation
Indices: 3352224--3352268 Score: 67
Period size: 17 Copynumber: 2.6 Consensus size: 18
3352214 AAAAATAGAA
*
3352224 AAAGAAAATGAAAACGAG
1 AAAGAAAATGAAAAAGAG
3352242 AAAGAAAA-GAAAAAGAG
1 AAAGAAAATGAAAAAGAG
3352259 AAA-AAAATGA
1 AAAGAAAATGA
3352269 GAGATGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 4 0.16
17 13 0.52
18 8 0.32
ACGTcount: A:0.73, C:0.02, G:0.20, T:0.04
Consensus pattern (18 bp):
AAAGAAAATGAAAAAGAG
Found at i:3352278 original size:29 final size:28
Alignment explanation
Indices: 3352190--3352270 Score: 69
Period size: 29 Copynumber: 2.8 Consensus size: 28
3352180 GAAAAAACAG
* *
3352190 AAGAAAAAAAAACAGAAGAA-GA-AAAAAA
1 AAGAAAAAGAAA-AGAA-AACGAGAAAGAA
3352218 ATAGAAAAAGAAAATGAAAACGAGAAAGAA
1 A-AGAAAAAGAAAA-GAAAACGAGAAAGAA
*
3352248 AAGAAAAAGAGAAA-AAAATGAGA
1 AAGAAAAAGA-AAAGAAAACGAGA
3352271 GATGAAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
28 12 0.27
29 24 0.53
30 9 0.20
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (28 bp):
AAGAAAAAGAAAAGAAAACGAGAAAGAA
Found at i:3360004 original size:18 final size:18
Alignment explanation
Indices: 3359981--3360089 Score: 146
Period size: 18 Copynumber: 6.1 Consensus size: 18
3359971 ATGTCAGATG
3359981 CCCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
*
3359999 CCCATGCTGGATCACTGC
1 CCCATGCTGGACCACTGC
* *
3360017 ACCATACTGGACCACTGC
1 CCCATGCTGGACCACTGC
* *
3360035 CCCATGCTGGATCACTAC
1 CCCATGCTGGACCACTGC
* * *
3360053 ACCATGTTGGACCACTGT
1 CCCATGCTGGACCACTGC
3360071 CCCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
3360089 C
1 C
3360090 TAATCCTCAC
Statistics
Matches: 75, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 75 1.00
ACGTcount: A:0.20, C:0.39, G:0.20, T:0.20
Consensus pattern (18 bp):
CCCATGCTGGACCACTGC
Found at i:3360030 original size:36 final size:36
Alignment explanation
Indices: 3359982--3360088 Score: 169
Period size: 36 Copynumber: 3.0 Consensus size: 36
3359972 TGTCAGATGC
3359982 CCATGCTGGACCACTGCCCCATGCTGGATCACTGCA
1 CCATGCTGGACCACTGCCCCATGCTGGATCACTGCA
* *
3360018 CCATACTGGACCACTGCCCCATGCTGGATCACTACA
1 CCATGCTGGACCACTGCCCCATGCTGGATCACTGCA
* * *
3360054 CCATGTTGGACCACTGTCCCATGCTGGACCACTGC
1 CCATGCTGGACCACTGCCCCATGCTGGATCACTGC
3360089 CTAATCCTCA
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 64 1.00
ACGTcount: A:0.21, C:0.38, G:0.21, T:0.21
Consensus pattern (36 bp):
CCATGCTGGACCACTGCCCCATGCTGGATCACTGCA
Found at i:3364414 original size:20 final size:20
Alignment explanation
Indices: 3364373--3364415 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
3364363 TCTAAGAGCC
*
3364373 CATTTAGGACTATTTAGATG
1 CATTTAGGACTATATAGATG
*
3364393 CATTTAGGAGC-ATATAGTTG
1 CATTTAGGA-CTATATAGATG
3364413 CAT
1 CAT
3364416 GTGGTAGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 19 0.95
21 1 0.05
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (20 bp):
CATTTAGGACTATATAGATG
Found at i:3364736 original size:18 final size:18
Alignment explanation
Indices: 3364713--3364819 Score: 169
Period size: 18 Copynumber: 5.9 Consensus size: 18
3364703 ATGTCAGATG
3364713 CCCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
*
3364731 CCCATGCTGGATCACTGC
1 CCCATGCTGGACCACTGC
*
3364749 ACCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
**
3364767 CCCATGCTGGATTACTGC
1 CCCATGCTGGACCACTGC
*
3364785 ACCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
3364803 CCCATGCTGGACCACTG
1 CCCATGCTGGACCACTG
3364820 ACCAATCCTC
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 79 1.00
ACGTcount: A:0.19, C:0.39, G:0.22, T:0.20
Consensus pattern (18 bp):
CCCATGCTGGACCACTGC
Found at i:3364756 original size:36 final size:36
Alignment explanation
Indices: 3364714--3364823 Score: 195
Period size: 36 Copynumber: 3.1 Consensus size: 36
3364704 TGTCAGATGC
3364714 CCATGCTGGACCACTGCCCCATGCTGGATCACTGCA
1 CCATGCTGGACCACTGCCCCATGCTGGATCACTGCA
*
3364750 CCATGCTGGACCACTGCCCCATGCTGGATTACTGCA
1 CCATGCTGGACCACTGCCCCATGCTGGATCACTGCA
*
3364786 CCATGCTGGACCACTGCCCCATGCTGGACCACTG-A
1 CCATGCTGGACCACTGCCCCATGCTGGATCACTGCA
3364821 CCA
1 CCA
3364824 ATCCTCACGA
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
35 4 0.06
36 67 0.94
ACGTcount: A:0.20, C:0.39, G:0.22, T:0.19
Consensus pattern (36 bp):
CCATGCTGGACCACTGCCCCATGCTGGATCACTGCA
Found at i:3368259 original size:21 final size:20
Alignment explanation
Indices: 3368233--3368271 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3368223 TAAGGCATTA
3368233 AACATCATAAACAAAACAAAT
1 AACATCATAAA-AAAACAAAT
*
3368254 AACATCATACAAAAACAA
1 AACATCATAAAAAAACAA
3368272 CCATCTAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.67, C:0.21, G:0.00, T:0.13
Consensus pattern (20 bp):
AACATCATAAAAAAACAAAT
Found at i:3369290 original size:30 final size:30
Alignment explanation
Indices: 3369250--3369310 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
3369240 TATTTGGTTT
*
3369250 AGCACTATAGTGTGTAAGGACACTTT-GTGC
1 AGCACCATAGTGTGTAAGGACA-TTTAGTGC
3369280 AGCACCATAGTGTGTAAGGACATTTAGTGC
1 AGCACCATAGTGTGTAAGGACATTTAGTGC
3369310 A
1 A
3369311 TATCGTGGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (30 bp):
AGCACCATAGTGTGTAAGGACATTTAGTGC
Found at i:3371712 original size:20 final size:21
Alignment explanation
Indices: 3371679--3371717 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
3371669 CTTATTTAGC
*
3371679 ATGAGTTTGCTTTGGATGATT
1 ATGAGTTTGCTTTGAATGATT
*
3371700 ATGA-TTTGTTTTGAATGA
1 ATGAGTTTGCTTTGAATGA
3371718 ATGATTTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.23, C:0.03, G:0.26, T:0.49
Consensus pattern (21 bp):
ATGAGTTTGCTTTGAATGATT
Found at i:3372231 original size:17 final size:17
Alignment explanation
Indices: 3372198--3372232 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3372188 AAGACCCATT
**
3372198 GTTCCTCTGTCGGACTC
1 GTTCCTCTGTCAAACTC
3372215 GTTCCTCTGTCAAACTC
1 GTTCCTCTGTCAAACTC
3372232 G
1 G
3372233 AATTGCCCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.11, C:0.34, G:0.20, T:0.34
Consensus pattern (17 bp):
GTTCCTCTGTCAAACTC
Found at i:3372948 original size:17 final size:17
Alignment explanation
Indices: 3372926--3372960 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3372916 AATTACATGC
3372926 ATATATATCATATATAT
1 ATATATATCATATATAT
* *
3372943 ATATATATTATATGTAT
1 ATATATATCATATATAT
3372960 A
1 A
3372961 ATAAAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (17 bp):
ATATATATCATATATAT
Found at i:3396650 original size:27 final size:28
Alignment explanation
Indices: 3396608--3396663 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
3396598 CTATTCCTTT
* *
3396608 CTTTTCTTTCATTTTC-TTGTTCTTAAAC
1 CTTTTCCTTCATTTTCATT-TCCTTAAAC
3396636 CTTTTCCTT-ATTTTCATTTCCTTAAAC
1 CTTTTCCTTCATTTTCATTTCCTTAAAC
3396663 C
1 C
3396664 ATTTATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.16, C:0.25, G:0.02, T:0.57
Consensus pattern (28 bp):
CTTTTCCTTCATTTTCATTTCCTTAAAC
Found at i:3401298 original size:2 final size:2
Alignment explanation
Indices: 3401236--3401397 Score: 133
Period size: 2 Copynumber: 88.5 Consensus size: 2
3401226 AAAAATATCA
3401236 AT AT A- AT AT A- AT AT A- AT AT A- AT AT A- AT AT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
3401271 AT -T A- AT A- AT AT AT AA AT -T AT AT -T AT AT A- AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3401307 -T GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
3401348 AT AT AT AT AT AT AT AT GT CAT ACT AC AC AT A- AT AT AT -T AT A-
1 AT AT AT AT AT AT AT AT AT -AT A-T AT AT AT AT AT AT AT AT AT AT
3401389 AT AT AT AT A
1 AT AT AT AT A
3401398 ATTTAATATT
Statistics
Matches: 132, Mismatches: 9, Indels: 38
0.74 0.05 0.21
Matches are distributed among these distances:
1 17 0.13
2 112 0.85
3 3 0.02
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3401511 original size:25 final size:27
Alignment explanation
Indices: 3401492--3401541 Score: 77
Period size: 25 Copynumber: 1.9 Consensus size: 27
3401482 AATATAATTT
3401492 ATAAATACCATAT-T-ATATATAAAGC
1 ATAAATACCATATATAATATATAAAGC
*
3401517 ATGAATACCATATATAATATATAAA
1 ATAAATACCATATATAATATATAAA
3401542 TATACCATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.55
26 1 0.05
27 9 0.41
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.32
Consensus pattern (27 bp):
ATAAATACCATATATAATATATAAAGC
Found at i:3410347 original size:21 final size:20
Alignment explanation
Indices: 3410314--3410357 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
3410304 ATTAGCTTGC
3410314 ATTTATAACCTCTTTATTACTT
1 ATTTATAACCTCTTT-TTA-TT
*
3410336 ATTT-TAATCTCTTTTTATT
1 ATTTATAACCTCTTTTTATT
3410355 ATT
1 ATT
3410358 CTTACAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 5 0.24
20 3 0.14
21 9 0.43
22 4 0.19
ACGTcount: A:0.25, C:0.14, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTTATAACCTCTTTTTATT
Found at i:3415102 original size:21 final size:21
Alignment explanation
Indices: 3415078--3415117 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3415068 TTAGAACAAA
3415078 TTTACAA-AAATCCTAAAAATG
1 TTTACAACAAAT-CTAAAAATG
*
3415099 TTTAGAACAAATCTAAAAA
1 TTTACAACAAATCTAAAAA
3415118 ACACTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.28
Consensus pattern (21 bp):
TTTACAACAAATCTAAAAATG
Found at i:3415267 original size:18 final size:18
Alignment explanation
Indices: 3415244--3415282 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3415234 AGGTGAAACA
*
3415244 AAAGAATTTTTTAG-AGAT
1 AAAGAACTTTTT-GTAGAT
3415262 AAAGAACTTTTTGTAGAT
1 AAAGAACTTTTTGTAGAT
3415280 AAA
1 AAA
3415283 AAGATAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 1 0.05
18 18 0.95
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.36
Consensus pattern (18 bp):
AAAGAACTTTTTGTAGAT
Found at i:3415285 original size:20 final size:18
Alignment explanation
Indices: 3415243--3415286 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
3415233 AAGGTGAAAC
3415243 AAAAGAATTTTTTAGAGA
1 AAAAGAATTTTTTAGAGA
* *
3415261 TAAAGAACTTTTTGTAGATA
1 AAAAGAA-TTTTT-TAGAGA
3415281 AAAAGA
1 AAAAGA
3415287 TAGATTTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 6 0.29
19 5 0.24
20 10 0.48
ACGTcount: A:0.50, C:0.02, G:0.16, T:0.32
Consensus pattern (18 bp):
AAAAGAATTTTTTAGAGA
Found at i:3420115 original size:23 final size:23
Alignment explanation
Indices: 3420085--3420134 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
3420075 CAAACACTAA
*
3420085 AACACTAAACGAACATGTTCGTG
1 AACACTAAACGAACACGTTCGTG
*
3420108 AACACTAAATGAACACGTTCGTG
1 AACACTAAACGAACACGTTCGTG
3420131 AACA
1 AACA
3420135 TACAAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.22, G:0.16, T:0.20
Consensus pattern (23 bp):
AACACTAAACGAACACGTTCGTG
Found at i:3422704 original size:22 final size:22
Alignment explanation
Indices: 3422676--3422719 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
3422666 TTTCTAGTCA
3422676 TTTGTAACT-TATGTAATTACAC
1 TTTGTAACTCT-TGTAATTACAC
3422698 TTTGTAACTCTTGTAATTACAC
1 TTTGTAACTCTTGTAATTACAC
3422720 GAACCACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.30, C:0.16, G:0.09, T:0.45
Consensus pattern (22 bp):
TTTGTAACTCTTGTAATTACAC
Found at i:3422745 original size:18 final size:20
Alignment explanation
Indices: 3422717--3422755 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
3422707 CTTGTAATTA
3422717 CACGAACCACAACCAC-AGC
1 CACGAACCACAACCACGAGC
*
3422736 CACG-ACCACATCCACGAGC
1 CACGAACCACAACCACGAGC
3422755 C
1 C
3422756 GACACGATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.36, C:0.49, G:0.13, T:0.03
Consensus pattern (20 bp):
CACGAACCACAACCACGAGC
Found at i:3429548 original size:23 final size:23
Alignment explanation
Indices: 3429504--3429554 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
3429494 ACGAACACTA
*
3429504 AAACACTAATCGAACATATTCGT
1 AAACACTAATCGAACACATTCGT
*
3429527 AAACACTAAAT-GAACACGTTCGT
1 AAACACT-AATCGAACACATTCGT
*
3429550 GAACA
1 AAACA
3429555 TATAAACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.45, C:0.22, G:0.12, T:0.22
Consensus pattern (23 bp):
AAACACTAATCGAACACATTCGT
Found at i:3442406 original size:25 final size:26
Alignment explanation
Indices: 3442356--3442408 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
3442346 AATTATCTTG
*
3442356 AATATTTAAATTAAATTAATTAAATA
1 AATATTTAAATTAAATTAAATAAATA
*
3442382 AATATTT-AATTAATTTAAA-ATAATA
1 AATATTTAAATTAAATTAAATA-AATA
3442407 AA
1 AA
3442409 ATCCATAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 1 0.04
25 16 0.67
26 7 0.29
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (26 bp):
AATATTTAAATTAAATTAAATAAATA
Found at i:3452194 original size:22 final size:25
Alignment explanation
Indices: 3452150--3452198 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
3452140 AATTATTCTG
3452150 AATATTTAACTTAAATTAATGAAATA
1 AATATTTAACTTAAATT-ATGAAATA
3452176 AATATTTAA-TT-AATT-TGAAATA
1 AATATTTAACTTAAATTATGAAATA
3452198 A
1 A
3452199 TAAAATCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.35
24 4 0.17
25 2 0.09
26 9 0.39
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (25 bp):
AATATTTAACTTAAATTATGAAATA
Found at i:3469635 original size:131 final size:131
Alignment explanation
Indices: 3469436--3469687 Score: 344
Period size: 131 Copynumber: 1.9 Consensus size: 131
3469426 TTTTGAGAAT
** * * * * *
3469436 GAAAATGATATTATCTAATTATTTACATTCGAGAATAAACGACCTCCCATGGCTTAAAGCAATAA
1 GAAAATGATAACATCTAATTATTTACAATCCAGAATAAAAGACCTCCCATGCCTTAAAGCAACAA
* * *
3469501 TTTATTACTCAAACCAAAATGAAGAGATATTACTATTTCATCTTAAAATTCAATATCGATCCAAG
66 TTTATTACTCAAACCAAAATGAAAAGATATCACTATTTCATCTTAAAAATCAATATCGATCCAAG
3469566 A
131 A
*
3469567 GAAAATGATAACATCTAATTATTT-CAAATCCAGAATAAAAGACCTCCCATGCCTTAAAGCAACC
1 GAAAATGATAACATCTAATTATTTAC-AATCCAGAATAAAAGACCTCCCATGCCTTAAAGCAACA
* *** *
3469631 ATTTATTACTCCAATTGAAATTAAAAGATATCACTATTTCATCTTAAAAATCAATAT
65 ATTTATTACTCAAACCAAAATGAAAAGATATCACTATTTCATCTTAAAAATCAATAT
3469688 TGAATCGAGT
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
130 1 0.01
131 103 0.99
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (131 bp):
GAAAATGATAACATCTAATTATTTACAATCCAGAATAAAAGACCTCCCATGCCTTAAAGCAACAA
TTTATTACTCAAACCAAAATGAAAAGATATCACTATTTCATCTTAAAAATCAATATCGATCCAAG
A
Found at i:3470916 original size:18 final size:17
Alignment explanation
Indices: 3470889--3470931 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
3470879 TATAGCCTGA
*
3470889 AAATAAAATAATAATAAT
1 AAATATAATAATAAT-AT
3470907 AAATATAATAATAATAT
1 AAATATAATAATAATAT
*
3470924 TAATATAA
1 AAATATAA
3470932 AAATGTCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATATAATAATAATAT
Found at i:3471785 original size:241 final size:241
Alignment explanation
Indices: 3471330--3472076 Score: 932
Period size: 243 Copynumber: 3.1 Consensus size: 241
3471320 TAACAAATTA
* * * * *
3471330 CCCGAAGGACTT-CCTAATTTTAGAAGTAGTTTACTAGGTAAGAAACTTTGGAAATTATTTTCTT
1 CCCGAATGACTTACC-AATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATTGTTTTCTT
* * *
3471394 ACTTTTTGAAAACTTCAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTTGAAAATCACAT
65 AC-TTTTCAAAATTTTAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTTGAAAA--ACAT
3471459 G-AAAACATCCTGCCCGAAGGTCTTATGGATGGTCCGAAAGACTTATCATCTTACTCGAAAGGCT
127 GTAAAACATCCTGCCCGAAGGTCTTATGGATGGTCCG-AAGACTTATCATCTTACTCGAAAGGCT
* * * *
3471523 TATAGATGACCCGAAGGATTTACTCACCATGCTCGAAAAACTTATTGAT-G
191 TATAGATGACTCGAAGGATTTACTCATCATGCTCGAAAGACTTAATGATGG
*
3471573 CCCGAATGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATCGTTTTCTTA
1 CCCGAATGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATTGTTTTCTTA
* * * * **
3471638 CTTTTCAAAATATTTTATTTTCATATTTAAATGATAAAATTTAATC-TTTTTT-AAAAACATGTA
66 CTTTTCAAAAT-TTTAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTTGAAAAACATGT-
* * * * *
3471701 AAAACATCCTGCCCGAAGGTCTTGTGGATAGTCTGAAGGACTTATCATCTTTCTCGAAATGCTTA
129 AAAACATCCTGCCCGAAGGTCTTATGGATGGTCCGAA-GACTTATCATCTTACTCGAAAGGCTTA
* * * * *
3471766 TATATGACTCGATGGATTTAGTCATCATGTTCGAGAGACTTAATGATGG
193 TAGATGACTCGAAGGATTTACTCATCATGCTCGAAAGACTTAATGATGG
* * * *
3471815 CTCAAATGACTTACCAATTTTGGAAATAGCTTACTAGTTAAGAAACTTT-AGAAATTGTTTTCTT
1 CCCGAATGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGA-AAATTGTTTTCTT
* * *
3471879 ACTTTTTAAAATTTTCAATTTTTAGATTTAAATGAGAAACTTTTCTCATTTTTTGAAAAACATTC
65 ACTTTTCAAAATTTT-AATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTTGAAAAACA-TG
* * * *
3471944 TAAAACATCATGCCCGAAGGTCTTATGGATGGCCCGATA-ATTTATCATCTTGCTCGAAAGGCTT
128 TAAAACATCCTGCCCGAAGGTCTTATGGATGGTCCGA-AGACTTATCATCTTACTCGAAAGGCTT
* * * *
3472008 ATAGATGACTCGAAGGATTTACTCATCATGCTTGAAAGGCTTACTAATGG
192 ATAGATGACTCGAAGGATTTACTCATCATGCTCGAAAGACTTAATGATGG
*
3472058 ACCGAATGACTTACCAATT
1 CCCGAATGACTTACCAATT
3472077 AAAAAACTTT
Statistics
Matches: 429, Mismatches: 63, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
239 5 0.01
240 2 0.00
241 103 0.24
242 107 0.25
243 169 0.39
244 40 0.09
245 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (241 bp):
CCCGAATGACTTACCAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTGAAAATTGTTTTCTTA
CTTTTCAAAATTTTAATTTTCAGATTTAAATGAGAAACTTTTCTCATTTTTTGAAAAACATGTAA
AACATCCTGCCCGAAGGTCTTATGGATGGTCCGAAGACTTATCATCTTACTCGAAAGGCTTATAG
ATGACTCGAAGGATTTACTCATCATGCTCGAAAGACTTAATGATGG
Found at i:3472009 original size:40 final size:41
Alignment explanation
Indices: 3471949--3472050 Score: 102
Period size: 40 Copynumber: 2.5 Consensus size: 41
3471939 CATTCTAAAA
* * *
3471949 CATCATGCCCG-AAGGTCTTATGGATGGCCCGATA-ATTTA-T
1 CATCATGCTCGAAAGG-CTTATAGATGACCCGA-AGATTTACT
* *
3471989 CATCTTGCTCGAAAGGCTTATAGATGACTCGAAGGATTTACT
1 CATCATGCTCGAAAGGCTTATAGATGACCCGAA-GATTTACT
*
3472031 CATCATGCTTGAAAGGCTTA
1 CATCATGCTCGAAAGGCTTA
3472051 CTAATGGACC
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
39 1 0.02
40 22 0.43
41 9 0.18
42 19 0.37
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (41 bp):
CATCATGCTCGAAAGGCTTATAGATGACCCGAAGATTTACT
Found at i:3478243 original size:24 final size:24
Alignment explanation
Indices: 3478213--3478260 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3478203 ACTCTTATTT
3478213 ATCAATCAACTTTGTTTGTAAGTC
1 ATCAATCAACTTTGTTTGTAAGTC
3478237 ATCAATCAACTTTGTTTGTAAGTC
1 ATCAATCAACTTTGTTTGTAAGTC
3478261 GTTGCCCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (24 bp):
ATCAATCAACTTTGTTTGTAAGTC
Found at i:3479448 original size:15 final size:15
Alignment explanation
Indices: 3479429--3479457 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3479419 GCACCCAAAA
3479429 AAAAAAT-TTCTTTT
1 AAAAAATATTCTTTT
3479443 AAAAAATATTCTTTT
1 AAAAAATATTCTTTT
3479458 TAATTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAAAATATTCTTTT
Done.